{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,11]],"date-time":"2025-09-11T16:59:39Z","timestamp":1757609979105,"version":"3.44.0"},"reference-count":54,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2025,9,3]],"date-time":"2025-09-03T00:00:00Z","timestamp":1756857600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:sec><jats:title>Introduction<\/jats:title><jats:p>Gut health is a critical determinant of poultry growth, immunity, and meat quality, with the intestinal barrier being fundamental to its maintenance. This study aimed to investigate the impacts of caged and cage-free rearing systems on the gut barrier of Lueyang black-bone chickens, specifically focusing on how these systems alter gut microbiota composition and metabolic profiles.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>Lueyang black-bone chickens were raised under either caged or cage-free conditions. Gut barrier integrity was assessed through histological examination of the duodenum and cecum. Microbial community structure was analyzed via 16S rRNA sequencing, and metabolic changes were profiled using LC\u2013MS-based non-targeted metabolomics.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Histological analysis revealed significantly greater intestinal wall thickness and higher goblet cell counts in the cage-free group (<jats:italic>p<\/jats:italic> &amp;lt; 0.0001). Microbiome sequencing showed that the caged group was enriched with fiber-degrading bacteria such as <jats:italic>Bacteroides<\/jats:italic> and <jats:italic>Rikenellaceae_RC9_gut_group<\/jats:italic>, while the cage-free group had a higher abundance of potential pathogens like <jats:italic>Acinetobacter<\/jats:italic> and <jats:italic>Campylobacter<\/jats:italic>. Metabolomics results indicated upregulation of bile acids and unsaturated fatty acids in the caged group, whereas phosphatidylcholine (PE) and lysophosphatidylcholine (LPC) were significantly elevated in the cage-free group. Further integrated analysis revealed strong positive correlations between Rikenellaceae_RC9_gut_group and bile acids, and between <jats:italic>Odoribacter<\/jats:italic>\/<jats:italic>Clostridia_UCG-014<\/jats:italic> and unsaturated fatty acids including traumatic acid.<\/jats:p><\/jats:sec><jats:sec><jats:title>Discussion<\/jats:title><jats:p>The findings suggest that caged rearing promoted a more beneficial microbial community structure, characterized by fiber-degrading bacteria that subsequently elevated anti-inflammatory and barrier-strengthening metabolites such as bile acids and unsaturated fatty acids. In contrast, the cage-free environment may predispose chickens to potential gut inflammation and barrier dysfunction, partly linked to higher levels of harmful bacteria and membrane phospholipid metabolites. These results highlight the role of rearing systems in modulating gut health through microbiota-metabolite interactions.<\/jats:p><\/jats:sec>","DOI":"10.3389\/fmicb.2025.1642169","type":"journal-article","created":{"date-parts":[[2025,9,3]],"date-time":"2025-09-03T12:34:19Z","timestamp":1756902859000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Multi-omics analysis of gut microbiota and metabolites reveals the effects of rearing systems on the duodenum and cecum gut barriers of lueyang black-bone chickens"],"prefix":"10.3389","volume":"16","author":[{"given":"Linqing","family":"Shao","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mingming","family":"Zhao","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shuang","family":"Zeng","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ling","family":"Wang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shanshan","family":"Wang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wenxian","family":"Zeng","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hongzhao","family":"Lu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2025,9,3]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"3070","DOI":"10.1016\/j.psj.2020.03.011","article-title":"Impact of different rearing systems on growth, carcass traits, oxidative stress biomarkers, and humoral immunity of broilers exposed to heat stress","volume":"99","author":"Abo Ghanima","year":"2020","journal-title":"Poult. Sci."},{"key":"ref2","doi-asserted-by":"publisher","first-page":"464","DOI":"10.3390\/pathogens13060464","article-title":"Recombinant bile salt hydrolase enhances the inhibition efficiency of Taurodeoxycholic acid against Clostridium perfringens virulence","volume":"13","author":"Alenezi","year":"2024","journal-title":"Pathogens"},{"key":"ref3","doi-asserted-by":"publisher","first-page":"101520","DOI":"10.1016\/j.psj.2021.101520","article-title":"Research note: effects of cage and floor rearing systems on growth performance, carcass traits, and meat quality in small-sized meat ducks","volume":"101","author":"Bai","year":"2022","journal-title":"Poult. Sci."},{"key":"ref4","doi-asserted-by":"publisher","first-page":"343","DOI":"10.1038\/ismej.2011.119","article-title":"Using network analysis to explore co-occurrence patterns in soil microbial communities","volume":"6","author":"Barber\u00e1n","year":"2012","journal-title":"ISME J."},{"key":"ref5","doi-asserted-by":"publisher","first-page":"159","DOI":"10.4172\/2329-8901.1000159","article-title":"Probiotic Lactobacillus species strengthen intestinal barrier function and tight junction integrity in experimental necrotizing enterocolitis","volume":"5","author":"Blackwood","year":"2017","journal-title":"J. Probiotics Health"},{"key":"ref6","doi-asserted-by":"publisher","first-page":"4707","DOI":"10.1038\/s41467-021-24983-z","article-title":"Salmonella effector SopD promotes plasma membrane scission by inhibiting Rab10","volume":"12","author":"Boddy","year":"2021","journal-title":"Nat. Commun."},{"key":"ref7","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1186\/s12866-024-03690-x","article-title":"Decoding the chicken gastrointestinal microbiome","volume":"25","author":"Burrows","year":"2025","journal-title":"BMC Microbiol."},{"key":"ref8","doi-asserted-by":"publisher","first-page":"344","DOI":"10.3389\/fmicb.2020.00344","article-title":"Contribution of epithelial apoptosis and subepithelial immune responses in Campylobacter jejuni-induced barrier disruption","volume":"11","author":"Butkevych","year":"2020","journal-title":"Front. Microbiol."},{"key":"ref9","doi-asserted-by":"publisher","first-page":"581","DOI":"10.1038\/nmeth.3869","article-title":"DADA2: high-resolution sample inference from Illumina amplicon data","volume":"13","author":"Callahan","year":"2016","journal-title":"Nat. Methods"},{"key":"ref10","doi-asserted-by":"publisher","first-page":"503","DOI":"10.1111\/j.1365-2982.2012.01921.x","article-title":"Intestinal barrier function in health and gastrointestinal disease","volume":"24","author":"Camilleri","year":"2012","journal-title":"Neurogastroenterol. Motil."},{"key":"ref11","doi-asserted-by":"publisher","first-page":"e76233","DOI":"10.1371\/journal.pone.0076233","article-title":"Lysophosphatidylcholine triggers TLR2- and TLR4-mediated signaling pathways but counteracts LPS-induced NO synthesis in peritoneal macrophages by inhibiting NF-\u03baB translocation and MAPK\/ERK phosphorylation","volume":"8","author":"Carneiro","year":"2013","journal-title":"PLoS One"},{"key":"ref12","doi-asserted-by":"publisher","first-page":"1471732","DOI":"10.3389\/fmicb.2024.1471732","article-title":"Unique rumen micromorphology and microbiota-metabolite interactions: features and strategies for Tibetan sheep adaptation to the plateau","volume":"15","author":"Chen","year":"2024","journal-title":"Front. Microbiol."},{"key":"ref13","doi-asserted-by":"publisher","first-page":"84","DOI":"10.3390\/ani8060084","article-title":"Free dietary choice and free-range rearing improve the product quality, gait score, and microbial richness of chickens","volume":"8","author":"Chen","year":"2018","journal-title":"Animals (Basel)"},{"key":"ref14","doi-asserted-by":"publisher","first-page":"7505","DOI":"10.3748\/wjg.v23.i42.7505","article-title":"Intestinal epithelium, intraepithelial lymphocytes and the gut microbiota - key players in the pathogenesis of celiac disease","volume":"23","author":"Cukrowska","year":"2017","journal-title":"World J. Gastroenterol."},{"key":"ref15","doi-asserted-by":"publisher","first-page":"430","DOI":"10.1080\/10408390701425615","article-title":"Antioxidant activity of proteins and peptides","volume":"48","author":"Elias","year":"2008","journal-title":"Crit. Rev. Food Sci. Nutr."},{"key":"ref16","doi-asserted-by":"publisher","first-page":"652","DOI":"10.3390\/jpm14060652","article-title":"The role of the gut microbiome in inflammatory bowel disease: the Middle East perspective","volume":"14","author":"El-Sayed","year":"2024","journal-title":"J. Pers. Med."},{"key":"ref17","doi-asserted-by":"publisher","first-page":"179","DOI":"10.3390\/nu11092179","article-title":"Docosahexaenoic and Eicosapentaenoic acids prevent altered-Muc2 secretion induced by palmitic acid by alleviating endoplasmic reticulum stress in LS174T goblet cells","volume":"11","author":"Escoula","year":"2019","journal-title":"Nutrients"},{"key":"ref18","doi-asserted-by":"publisher","first-page":"38303","DOI":"10.1038\/srep38303","article-title":"Genomic variations leading to alterations in cell morphology of Campylobacter spp","volume":"6","author":"Esson","year":"2016","journal-title":"Sci. Rep."},{"key":"ref19","doi-asserted-by":"publisher","first-page":"222","DOI":"10.3390\/microorganisms9112222","article-title":"Enterococcus spp.: is it a bad choice for a good use-a conundrum to solve?","volume":"9","author":"Ferchichi","year":"2021","journal-title":"Microorganisms"},{"key":"ref20","doi-asserted-by":"publisher","first-page":"658354","DOI":"10.3389\/fimmu.2021.658354","article-title":"Impact of bacterial metabolites on gut barrier function and host immunity: a focus on bacterial metabolism and its relevance for intestinal inflammation","volume":"12","author":"Gasaly","year":"2021","journal-title":"Front. Immunol."},{"key":"ref21","doi-asserted-by":"publisher","first-page":"1463","DOI":"10.1016\/j.jcmgh.2021.02.007","article-title":"Regulation of intestinal barrier function by microbial metabolites","volume":"11","author":"Ghosh","year":"2021","journal-title":"Cell. Mol. Gastroenterol. Hepatol."},{"key":"ref22","doi-asserted-by":"publisher","first-page":"1217820","DOI":"10.3389\/frmbi.2023.1217820","article-title":"Anthracyclines and trastuzumab associated cardiotoxicity: is the gut microbiota a friend or foe?\u2013a mini-review","volume":"2","author":"Gon\u00e7alves-Nobre","year":"2023","journal-title":"Front. Microbiolomes"},{"key":"ref23","doi-asserted-by":"publisher","first-page":"4","DOI":"10.1186\/s13099-019-0283-z","article-title":"Campylobacter jejuni enters gut epithelial cells and impairs intestinal barrier function through cleavage of occludin by serine protease HtrA","volume":"11","author":"Harrer","year":"2019","journal-title":"Gut Pathog."},{"key":"ref24","doi-asserted-by":"publisher","first-page":"409","DOI":"10.3390\/biom13030409","article-title":"Molecular targets in Campylobacter infections","volume":"13","author":"Heimesaat","year":"2023","journal-title":"Biomolecules"},{"key":"ref25","doi-asserted-by":"publisher","first-page":"556","DOI":"10.1016\/j.aninu.2020.07.009","article-title":"Lysine deficiency impaired growth performance and immune response and aggravated inflammatory response of the skin, spleen and head kidney in grown-up grass carp (Ctenopharyngodon idella)","volume":"7","author":"Hu","year":"2021","journal-title":"Anim. Nutr."},{"key":"ref26","doi-asserted-by":"publisher","first-page":"85","DOI":"10.3390\/ani9121085","article-title":"The role of housing environment and dietary protein source on the gut microbiota of chicken","volume":"9","author":"Hubert","year":"2019","journal-title":"Animals (Basel)"},{"key":"ref27","doi-asserted-by":"publisher","first-page":"34154","DOI":"10.1007\/s11356-021-13986-4","article-title":"Type 3 secretion system 1 of Salmonella Typhimurium and its inhibitors: a novel strategy to combat salmonellosis","volume":"28","author":"Hussain","year":"2021","journal-title":"Environ. Sci. Pollut. Res. Int."},{"key":"ref28","doi-asserted-by":"publisher","first-page":"1021","DOI":"10.1007\/s11745-016-4174-5","article-title":"Traumatic acid reduces oxidative stress and enhances collagen biosynthesis in cultured human skin fibroblasts","volume":"51","author":"Jab\u0142o\u0144ska-Trypu\u0107","year":"2016","journal-title":"Lipids"},{"key":"ref29","doi-asserted-by":"publisher","first-page":"e13514","DOI":"10.14814\/phy2.13514","article-title":"Lactobacillus reuteri strains protect epithelial barrier integrity of IPEC-J2 monolayers from the detrimental effect of enterotoxigenic Escherichia coli","volume":"6","author":"Karimi","year":"2018","journal-title":"Physiol. Rep."},{"key":"ref30","doi-asserted-by":"publisher","first-page":"113153","DOI":"10.1016\/j.celrep.2023.113153","article-title":"Commensal bacteria signal through TLR5 and AhR to improve barrier integrity and prevent allergic responses to food","volume":"42","author":"Kemter","year":"2023","journal-title":"Cell Rep."},{"key":"ref31","doi-asserted-by":"publisher","first-page":"e0045522","DOI":"10.1128\/msystems.00455-22","article-title":"Identification and characterization of major bile acid 7\u03b1-Dehydroxylating Bacteria in the human gut","volume":"7","author":"Kim","year":"2022","journal-title":"mSystems"},{"key":"ref32","doi-asserted-by":"publisher","first-page":"793","DOI":"10.1172\/jci.insight.153793","article-title":"Disruption of the crypt niche promotes outgrowth of mutated colorectal tumor stem cells","volume":"7","author":"Klingler","year":"2022","journal-title":"JCI Insight"},{"key":"ref33","doi-asserted-by":"publisher","first-page":"304149","DOI":"10.1155\/2015\/304149","article-title":"Enterococcus faecium NCIMB 10415 modulates epithelial integrity, heat shock protein, and proinflammatory cytokine response in intestinal cells","volume":"2015","author":"Klingspor","year":"2015","journal-title":"Mediat. Inflamm."},{"key":"ref34","doi-asserted-by":"publisher","first-page":"1784","DOI":"10.1126\/science.275.5307.1784","article-title":"Constitutive transcriptional activation by a beta-catenin-Tcf complex in APC\u2212\/\u2212 colon carcinoma","volume":"275","author":"Korinek","year":"1997","journal-title":"Science"},{"key":"ref9001","doi-asserted-by":"publisher","first-page":"1421","DOI":"10.1007\/s00253-015-7039-6.","article-title":"Denitrifying sulfide removal process on high-salinity wastewaters in the presence of Halomonas sp","volume":"100","author":"Liu","year":"2016","journal-title":"Appl Microbiol Biotechnol"},{"key":"ref35","doi-asserted-by":"publisher","first-page":"2782","DOI":"10.1002\/jsfa.6099","article-title":"Isolation and identification of antioxidative peptides from pilot-scale black-bone silky fowl (Gallus gallus domesticus Brisson) muscle oligopeptides","volume":"93","author":"Liu","year":"2013","journal-title":"J. Sci. Food Agric."},{"key":"ref36","doi-asserted-by":"publisher","first-page":"299","DOI":"10.3389\/fmicb.2019.00299","article-title":"Lactobacillus plantarum ZS2058 and Lactobacillus rhamnosus GG use different mechanisms to prevent Salmonella infection in vivo","volume":"10","author":"Liu","year":"2019","journal-title":"Front. Microbiol."},{"key":"ref37","doi-asserted-by":"publisher","first-page":"e0235223","DOI":"10.1128\/spectrum.02352-23","article-title":"Investigating the cecal microbiota of broilers raised in extensive and intensive production systems","volume":"11","author":"Marcolla","year":"2023","journal-title":"Microbiol. Spectr."},{"key":"ref38","doi-asserted-by":"publisher","first-page":"2232","DOI":"10.1136\/gutjnl-2020-322260","article-title":"Mucus barrier, mucins and gut microbiota: the expected slimy partners?","volume":"69","author":"Paone","year":"2020","journal-title":"Gut"},{"key":"ref39","doi-asserted-by":"publisher","first-page":"277","DOI":"10.3389\/fimmu.2019.00277","article-title":"Short chain fatty acids (SCFAs)-mediated gut epithelial and immune regulation and its relevance for inflammatory bowel diseases","volume":"10","author":"Parada Venegas","year":"2019","journal-title":"Front. Immunol."},{"key":"ref40","doi-asserted-by":"publisher","first-page":"136","DOI":"10.1007\/s00284-022-02828-2","article-title":"Effects of growth stage and rearing pattern on pig gut microbiota","volume":"79","author":"Qi","year":"2022","journal-title":"Curr. Microbiol."},{"key":"ref41","doi-asserted-by":"publisher","first-page":"339","DOI":"10.1016\/j.plefa.2013.02.001","article-title":"Effect of eicosapentaenoic acid-derived prostaglandin E3 on intestinal epithelial barrier function","volume":"88","author":"Rodr\u00edguez-Lagunas","year":"2013","journal-title":"Prostaglandins Leukot. Essent. Fatty Acids"},{"key":"ref42","doi-asserted-by":"publisher","first-page":"S12","DOI":"10.1097\/MCG.0b013e31826ae849","article-title":"The gut barrier: new acquisitions and therapeutic approaches","volume":"46","author":"Scaldaferri","year":"2012","journal-title":"J. Clin. Gastroenterol."},{"key":"ref43","doi-asserted-by":"publisher","first-page":"7537","DOI":"10.1128\/aem.01541-09","article-title":"Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities","volume":"75","author":"Schloss","year":"2009","journal-title":"Appl. Environ. Microbiol."},{"key":"ref44","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1093\/gastro\/goy052","article-title":"Fight them or feed them: how the intestinal mucus layer manages the gut microbiota","volume":"7","author":"Schroeder","year":"2019","journal-title":"Gastroenterol. Rep. (Oxf)"},{"key":"ref45","first-page":"309","article-title":"Gut failure in critical care: old school versus new school","volume":"28","author":"Sertaridou","year":"2015","journal-title":"Ann. Gastroenterol."},{"key":"ref46","doi-asserted-by":"publisher","first-page":"515","DOI":"10.1016\/j.foodres.2015.08.008","article-title":"Influence of the growth morphology on the behavior of Salmonella typhimurium and Listeria monocytogenes under osmotic stress","volume":"77","author":"Smet","year":"2015","journal-title":"Food Res. Int."},{"key":"ref47","doi-asserted-by":"publisher","first-page":"401","DOI":"10.1016\/j.mib.2008.09.008","article-title":"Therapeutic potential of type a (I) lantibiotics, a group of cationic peptide antibiotics","volume":"11","author":"Smith","year":"2008","journal-title":"Curr. Opin. Microbiol."},{"key":"ref48","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1016\/j.cmet.2016.05.005","article-title":"Intestinal crosstalk between bile acids and microbiota and its impact on host metabolism","volume":"24","author":"Wahlstr\u00f6m","year":"2016","journal-title":"Cell Metab."},{"key":"ref49","doi-asserted-by":"publisher","first-page":"159","DOI":"10.1080\/03079450500112195","article-title":"Intercurrent coccidiosis and necrotic enteritis of chickens: rational, integrated disease management by maintenance of gut integrity","volume":"34","author":"Williams","year":"2005","journal-title":"Avian Pathol."},{"key":"ref50","doi-asserted-by":"publisher","first-page":"653","DOI":"10.1177\/1753425920966686","article-title":"Docosahexaenoic acid alleviates cell injury and improves barrier function by suppressing necroptosis signalling in TNF-\u03b1-challenged porcine intestinal epithelial cells","volume":"26","author":"Xiao","year":"2020","journal-title":"Innate Immun."},{"key":"ref51","doi-asserted-by":"publisher","first-page":"372","DOI":"10.1016\/j.immuni.2013.08.003","article-title":"Tryptophan catabolites from microbiota engage aryl hydrocarbon receptor and balance mucosal reactivity via interleukin-22","volume":"39","author":"Zelante","year":"2013","journal-title":"Immunity"},{"key":"ref52","doi-asserted-by":"publisher","first-page":"898","DOI":"10.3390\/genes13101898","article-title":"Effects of different rearing systems on Lueyang black-bone chickens: meat quality, amino acid composition, and breast muscle transcriptome","volume":"13","author":"Zhang","year":"2022","journal-title":"Genes (Basel)"},{"key":"ref53","doi-asserted-by":"publisher","first-page":"1330","DOI":"10.3390\/nu16091330","article-title":"Nano-selenium alleviates cd-induced chronic colitis through intestinal Flora","volume":"16","author":"Zhou","year":"2024","journal-title":"Nutrients"}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2025.1642169\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,9,3]],"date-time":"2025-09-03T12:34:20Z","timestamp":1756902860000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2025.1642169\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,9,3]]},"references-count":54,"alternative-id":["10.3389\/fmicb.2025.1642169"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2025.1642169","relation":{},"ISSN":["1664-302X"],"issn-type":[{"type":"electronic","value":"1664-302X"}],"subject":[],"published":{"date-parts":[[2025,9,3]]},"article-number":"1642169"}}